My method has been to complete the return, run the regular diagnostics, make any corrections needed then without putting in the date signed on Form 8879, create the efile. This will assign a DCN (declaration Control Number), run the diagnostics and give you the notice that the date of signature must be input. Then I create a pdf to send with a password to my clients (virtually no one does this in my home office) and instruct the client to review the returns, print out the 8879, sign and fax or mail to me. They could also scan and email but I always warn that it should be encrypted or protected somehow. They can also upload to my website if comfortable (it is secure but a bit more complicated than faxing).
When I receive the signed 8879, I input the date signed and recreate the efile and send. I also update several times daily for reasons stated earlier.
Fro 2009 tax year, I also stated with the emailed return that I would not be sending a paper return unless specifically requested. I do, however, send Form 9325 showing the date received by IRS and how to contact IRS with issues of delay, etc. I also send my bill at that time because, although my engagement letter states that payment is due upon receipt of the return, I bill when it is accepted. But that's me...